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Selective breeding: the process of breeding plants and animals for particular genetic traits

recombinant deoxyribonucleic acid: genetically engineered DNA made by recombining fragments of DNA from different organisms

Genetic Engineering- The group of techniques of genetics and biotechnology used to cut up and join together genetic material and especially DNA from one or more species of organism and to introduce the result into an organism in order to change one or more of its characteristics.

Scientific alteration of the structure of genetic material in a living organism. It involves the production and use of recombinant DNA.

Here are some genetically altered organisms:

This chicken above is not a joke, Go to http://www.newscientist.com/article/dn2307-featherless-chicken-creates-a-flap.html for more information on the featherless chicken which is shown above. 

This video was made by a 9th grader for her biology class, and it explains the general process of genetic engineering very well. I found it helpful. 

Bacterial Conjugation- The transfer of genetic material from an F+ to an F- cell. Genetic material is passed through a thin tube-like structure on the surface of the F+, cell called the F pilus. F+ cells are reffered to as having an F factor, the fertility plasmid that allows the donor cell to conjugate with the recipient via the F pilus. (Bacteria Sex)

Plasmid- A circular, double-stranded unit of DNA that replicates within a cell independently of the chromosomal DNA. Plasmids are often found in bacteria and are used in recombinant DNA research to transfer genes between cells.

          - Small (a few thousand base pairs)

          - Usually carry only a few genes

          - Have a single origin of replication

          - Usually carry antibiotic properties

Examples:

DNA Palindromes- A DNA or RNA sequence which reads the same in both directions. The sites of many restriction enzymes that cut (restrict) DNA are palindromes.

Restriction enzymes are DNA-cutting enzymes found in bacteria (and harvested from them for use). Because they cut within the molecule, they are often called restriction endonucleases.

In order to be able to sequence DNA, it is first necessary to cut it into smaller fragments. Many DNA-digesting enzymes (like those in your pancreatic fluid) can do this, but most of them are no use for sequence work because they cut each molecule randomly. This produces a heterogeneous collection of fragments of varying sizes. What is needed is a way to cleave the DNA molecule at a few precisely-located sites so that a small set of homogeneous fragments are produced. The tools for this are the restriction endonucleases. The rarer the site it recognizes, the smaller the number of pieces produced by a given restriction endonuclease.

This video does a terrific job explains hoow and why restriction enzymes function the way they do.

A restriction enzyme recognizes and cuts DNA only at a particular sequence of nucleotides. For example, the bacterium Hemophilus aegypticus produces an enzyme named HaeIII that cuts DNA wherever it encounters the sequence

5'GGCC3'

3'CCGG5'

 

  This shows the DNaA being cut to the exact measurement by the restriction enzyme, and then being attached with the other cut foreign DNA.  The restriction enzyme allows for the two DNA strands to fit together PERFECTLY.

Transgenic Organism - An organism with DNA from two different places (plasmid, gene) that is combined and stuck into a new organism. Creating the transgenic organism.

The Plant that is created above is an example of a transgenic organism.

 

Cleavage - Where the nonrestrictive enzyme cuts the DNA/Plasmid.

Sticky Ends- Non-blunt ends are created by various overhangs. An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. These overhangs are in most cases palindromic.

 

VNTR stands for "Variable Number of Tandem Repeats." It is polymorphic, meaning that it comes in many different forms. The number of tandem repeats of a particular sequence varies greatly within a given population because everyone's is unique (with the exception of identical twins because they have identical DNA). 

     Each band in a VTNR scan must come from either the subject's mother or its father and the smallest bands travel more quickly than larger bands. Because the subject's mother is obvious at birth, the VTNR scan in primarily used in paternity testing. Each band must be identified as coming from either the mother or father in order for a father to be determined to actually be the baby's father.

     Another common use for VNTR is in criminal cases for DNA evidence. Recently, many prisoners have been determined to be innocent when prosecutors reexamine the DNA

 evidence using VTNR. They may be innocent if their DNA does not match the DNA on the evidence from their cases. Dr. Henry Lee was a famous advocate of this procedure. 

 

 

13.1 Changing the Living World

 

 

·         selective breeding- method of improving a species by allowing only those individual organisms with desired characteristics to produce the next generation

·         hybridization- breeding technique that involves crossing dissimilar individuals to bring together the best traits of both organisms

·         inbreeding- continued breeding of individuals with similar characteristics

·         polyploid- having many sets of chromosomes

·         humans use selective breeding to pass desired traits on to the next generation of organisms

·         breeders can increase the genetic variation in  a population by inducing mutations, which are the ultimate source of genetic variability

http://www.slic2.wsu.edu:82/hurlbert/micro101/images/LigaseAnimation6.gif

Above is a link for an animation displaying how recombinant DNA is formed, especially highlighting the fact that sticky ends have overhangs which aid the process of gene splicing immensley.

 

There has been lots of talk surrounding gene splicing. Gene splicing is the process of chemically cutting DNA in order to add bases to the DNA strand. The DNA is cut using special chemicals called restriction enzymes, which there are thousands of, and each one has its own, unique and specific code of DNA that it can cut. In other words, gene splicing is taking pieces of DNA from one or more organisms then combining them to create new DNA. taking pieces of DNA from one or more organisms then combining them to create new DNA.

 

Clone: descendents derived asexually from a single individual through cuttng or transfering of genes into the offspring

 

 

 

 

 

Somatic Cell

 

Are any cells forming the body of an organism, as opposed to germline cells. In mammals germline cells  are the spermatozoa and ova which fuse during fertilization to produce a cell called a zygote from which the entire mammalian embryo develops. Every other cell type in the mammalian body—apart from the sperm and ova, the cells from which they are made and undifferentiated stem cells—is a somatic cell: internal organs, skin, bones, blood, and connective tissue are all made up of somatic cells.

 

 Here is a picture of a stomatic cell during cloning.

 

 

 

Gene Therapy

 

Is the insertion of genes into an individual's cells and tissues to treat a disease, such as a hereditary disease in which a deleterious mutant allele is replaced with a functional one. Although the technology is still in its infancy, it has been used with some success. Scientific breakthroughs continue to move gene therapy toward mainstream medicine.

The correction of a genetic deficiency in a cell by the additon of new DNA and its insertion into the genome.  

 A picture showing the process of Gene Therapy

 

 

Here is a video explaning the process of Gene Therapy through a live cell.

 

 

 

PCR (Polymerase Chain Reaction)

 

Is a technique to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. The method relies on thermal cycling, consisting of cycles of repeated heating and cooling of the reaction for DNA melting and enzymatic replication of the DNA.  Short DNA fragments containing sequences complementary to the target region along with a DNA polymerase (after which the method is named) are key components to enable selective and repeated amplification. As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the DNA template is a

mplified.

 

The Polymerase Chain Reaction begins with a single strand of DNA. It denature when it is heated, then cooled to about 60 degrees to allow the primers to form hydrogen bonds. Then, at about 70 degrees, the DNA polymerase adds nucleotides to add the 3' end of each primer.

 

This PCR is applicable in numerous real life situations, mostly those in the forensic science field. They include, but are not limited to, identifying fossils, diagnosing prenatal diseases, paternity testing, and can determine if a gene mutation in present in a given subject.

The "ingredients" of the PCR are 3 nucleotides, primers, and tap polymerase. The tap polymerase is used because it can tolerate the heat of the reaction. This reaction follows all the base pair rules, so A goes with T, and C goes with G. It is about a 3 hour cycle. Also, it repeats 20-30 times to produce as many DNA samples necessary for the application. 

The DNA strands increase in each cycle that is completed. For example, after 2 cycles, 4 strands of the target DNA are produced per DNA strand that you started with. After 3 cycles, there are 8 strands produced. As you increase the number of cycles, the number of strands produced is doubled. In the end of the reaction, about 33 million copies of the ta

 

rget DNA are produced. 

 

This is a helpful diagram of the Polymerase Chain Reaction.

 

Here is an interesting video explaning what PCR is and how it works:

 

 

 

Gel Electrophoresis

 

is a technique used for the separation of DNA, RNA, or protein molecules using an electric field applied to a gel matrix. DNA Gel electrophoresis is usually performed for analytical purposes, often after amplification of DNA via PCR, but may be used as a preparative technique prior to use of other methods such as mass spectrometry, RFLP, PCR, cloning, DNA sequencing, or Southern blotting for further characterization.

 

 

 A picture of gel electrophoresis.

 

 

this is a great diagram of the steps in Gel Elctrophoresis 

 

HEre is a video showing how Gel Electrophoresis is used.

 

DESIGNER BABIES:

 

What is a designer baby?

Advanced reproductive technologies allow parents and doctors to screen embryos for genetic disorders and select healthy embryos.   In-vitro fertilisation or IVF The fear is that in the future we may be able to use genetic technologies to modify embryos and choose desirable or cosmetic characteristics. Designer babies is a term used by journalists to describe this frightening scenario. It is not a term used by scientists. Advanced reproductive techniques involve using InVitro Fertilisation or IVF to fertilise eggs with sperm in 'test-tubes' outside the mother's body in a laboratory. These techniques allow doctors and parents to reduce the chance that a child will be born with a genetic disorder. At the moment it is only legally possible to carry out two types of advanced reproductive technologies on humans. The first involves choosing the type of sperm that will fertilise an egg: this is used to determine the sex and the genes of the baby. The second technique screens embryos for a genetic disease: only selected embryos are implanted back into the mother's womb. This is called Pre-implantation Genetic Diagnosis (PGD). Recently scientists have made rapid advances in our knowledge of the human genome and in our ability to modify and change genes. In the future we may be able to "cure" geneticy diseases in embryos by replacing faulty sections of DNA with healthy DNA. This is called germ line therapy and is carried out on an egg, sperm or a tiny fertilised embryo. Such therapy has successfully been done on animal embryos but at present it is illegal to do this in humans. However, it is legal to modify the faulty genes in the cells of a grown child or an adult to cure diseases like cystic fibrosis - this is called body cell gene therapy.

 

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Genetically modified food

 

 

Genetically modified (GM) foods are foods derived from genetically modified organisms. Genetically modified organisms have had specific changes introduced into their DNA by genetic engineering, using a process of either Cisgenesis or Transgenesis. These techniques are much more precise than mutagenesis (mutation breeding) where an organism is exposed to radiation or chemicals to create a non-specific but stable change. Other techniques by which humans modify food organisms include selective breeding (plant breeding and animal breeding), and somaclonal variation.

GM foods were first put on the market in the early 1990s. Typically, genetically modified foods are transgenic plant products: soybean, corn, canola, and cotton seed oil. But animal products have also been developed. In 2006 a pig was controversially^[1][2] engineered to produce omega-3 fatty acids through the expression of a roundworm gene produced.^[3] Researchers have also developed a genetically-modified breed of pigs that are able to absorb plant phosphorus more efficiently, and as a consequence the phosphorus content of their manure is reduced by as much as 60%. ^[4]

Critics have objected to GM foods on several grounds, including perceived safety issues,^[5] ecological concerns, and economic concerns raised by the fact that these organisms are subject to intellectual property law.

 

Dangers of Genetically Modified Foods:

• Certain studies show that GM foods can be detremental to the immune system and vital organs
• GM foods also show evidence of causing cancer in some people
• Stomach lesions have been found in those who were subject to test genetically modified foods
• There is also the threat that these GM foods could cause deadly allergic reactions in some

This is a very informative video on the health threats of GM foods

 

Method

Genetic modification involves the insertion or deletion of genes. In the process of Cisgenesis genes are artificially transferred between organisms that could be conventionally bred. In the process of Transgenesis genes from a different species are inserted, which is a form of horizontal gene transfer. In nature this can occur when exogenous DNA penetrates the cell membrane for any reason. To do this artificially may require attaching the genes to a virus or just physically inserting the extra DNA into the nucleus of the intended host with a very small syringe, or with very small particles fired from a gene gun. However, other methods exploit natural forms of gene transfer, such as the ability of Agrobacterium to transfer genetic material to plants, and the ability of lentiviruses to transfer genes to animal cells.

 

 

Polymerase Chain Reaction --- PCR

 

     This process is used in order to take a small sample of DNA and make more.  This is used when there is a small sample of DNA, but a greater sample is needed in order to run tests.  For example, if there is a crime commited and DNA is needed to identify a suspect, but there is only a small sample of DNA found at the crime scene.  Since more is needed to run the forensics tests, PCR is used to make more identical DNA from which test could be run.

 

     PCR is extremley usefull beacuse it does not require the use of a live cell to reproduce the DNA.  Instead the DNA is heated to a very high temperature until it is denatured.  At this point the hydrogen bonds break and the DNA splits into two.  The temperature is than decreased and nucleotides and Polymerase are added in order to add pairs to each of the single strands.  Now that there are two DNA strands from one, they are heated and denatured again and the process is repeated.  This is so effective that after 25 repetitions there are 33,554,432 DNA, from the one.

 

     However a regular polymerase that the human body uses cannot be used.  Because of the hot temperatures, a different polymerase needs to be used.

 

This picture shows polymerase found in the bacteria called Thermus aquaticus.  This polymerase is important because it was found in a hot spring, so it is effective to work in temperatures of 75-80 degrees celcius.  This way it doesnt get denatured in the hot temperatures that were used to denature the DNA to make it split.

 

     Gel electrophoresis

 

          This is a process used to seperate DNA fragments by their length. 

 

       There are not many things that are needed in order to perform gel electrophoresis.  A gell is needed as a "filter" for the DNA.  A positive and negative charge is also needed.  Buffer is needed, along with wells in the gel, and a ladder sample is recommended.

 

     The gel has wells in it in order to put DNA samples into.  The samples all start off in the same area so that the results are the same.  The gel is placed into a buffer solution inside of a container.  The wells must be placed near the negative charge, because the DNA has a negative charge.  This way the DNA goes towards the positive end.

 

     After the charge is run for about an hour, the gel is examined.  The gel is put under a special light that makes the samples glow (they glow because of the dye added to them).  The samples that are further down the gel are shorter because they made it further, quicker.  The ladder now comes in handy because it has samples with lengths that have been figured out before.  This makes it easy to compare the lengths of the samples to the lengths that are already known, which makes for a good estimate.

 

   This is a good example of gel electrophoresis.  On the right there is a ladder set up so that the samples to the left could be estimated in length.  The samples farther away from the wells are shorter and the samples closer to the wells are longer.

Using the Knowledge of Gel Electrophoresis and PCR, scientists can apply it to a process called DNA fingerprinting: Individual identification through the use of multilocus genotyping. The process of DNA fingerprinting can be shown through this diagram:

Now the scientists have a  tray that will compare the DNA  from the crime scene to the DNA  from the suspect. PCR comes into play because it allows scientists to make numerous copys of isolated DNA.